Since whole-genome sequencing of many crops has been achieved, crop functional genomics studies have stepped into the big-data and high-throughput era. However, acquisition of large-scale phenotypic data has become one of the major bottlenecks hindering crop breeding and functional genomics studies. Nevertheless, recent technological advances provide us potential solutions to relieve this bottleneck and to explore advanced methods for large-scale phenotyping data acquisition and processing in the coming years. In this article, we review the major progress on high-throughput phenotyping in controlled environments and field conditions as well as its use for post-harvest yield and quality assessment in the past decades. We then discuss the latest multi-omics research combining high-throughput phenotyping with genetic studies. Finally, we propose some conceptual challenges and provide our perspectives on how to bridge the phenotype–genotype gap. It is no doubt that accurate high-throughput phenotyping will accelerate plant genetic improvements and promote the next green revolution in crop breeding.

由于已经实现了许多农作物的全基因组测序，因此农作物功能基因组学研究已进入大数据和高通量时代。然而，大规模表型数据的获取已成为阻碍作物育种和功能基因组学研究的主要瓶颈之一。尽管如此，最新的技术进步为我们提供了解决这一瓶颈的潜在解决方案，并在未来几年内探索了用于大规模表型数据采集和处理的先进方法。在本文中，我们回顾了过去几十年来在受控环境和田间条件下高通量表型的主要进展及其在收获后产量和质量评估中的应用。然后，我们讨论结合高通量表型和遗传研究的最新多组学研究。最后，我们提出了一些概念上的挑战，并就如何弥合表型-基因型差距提供了观点。毫无疑问，准确的高通量表型将加速植物遗传改良，并促进作物育种的下一次绿色革命。